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## I

IBioAdaptable - Interface in org.thalia.bio
IBioAdapter - Interface in org.thalia.bio
IBioAllele - Interface in org.thalia.bio
  Class Description Here
IBioConstants - Interface in org.thalia.bio.entity
  Class Description Here
IBioCross - Interface in org.thalia.bio
  Class Description Here
IBioCrossTypes - Interface in org.thalia.bio
  Class Description Here
IBioEntity - Interface in org.thalia.bio
  Class Description Here
IBioEntityTypes - Interface in org.thalia.bio
  Class Description Here
IBioGenome - Interface in org.thalia.bio
IBioGenomeProperties - Interface in org.metaqtl
  This interface defines both the keys and the default values of properties which can be handled by a org.thalia.bio.entity.IBioGenome.
IBioIndividual - Interface in org.thalia.bio
  Class Description Here
IBioIndividualTree - Interface in org.thalia.bio
  Class Description Here
IBioLGroup - Interface in org.thalia.bio
IBioLGroupProperties - Interface in org.metaqtl
  This interface defines the key of properties which can be handled by a org.thalia.bio.entity.IBioLGroup.
IBioLocus - Interface in org.thalia.bio
IBioLocusProperties - Interface in org.metaqtl
  This interface defines the key of the properties which can be handled by a org.thalia.bio.entity.IBioLocus.
IBioOntology - Interface in org.thalia.bio
  This interface defines some rules to handle a ontology.
IBioOntologyTerm - Interface in org.thalia.bio
  This class defines a term of an ontology.
IBioPopulation - Interface in org.thalia.bio
  Class Description Here
ic1 - Variable in class org.metaqtl.Qtl.QTLSupport
  The recombination rate between the QTL position and the left border of the IC.
ic2 - Variable in class org.metaqtl.Qtl.QTLSupport
  The recombination rate between the QTL position and the right border of the IC.
ICOMP - Static variable in class org.metaqtl.EMCriteria
icomp - Variable in class org.metaqtl.EMCriteria
ICOMP_NAME - Static variable in class org.metaqtl.EMCriteria
id - Variable in class org.metaqtl.Qtl
  The id of the Qtl
id - Variable in class org.thalia.bio.entity.bean.OntologyTermBean
  The id of the term.
idx - Variable in class org.metaqtl.TreeNode
  ? The identifiant of the cluster.
idx1 - Variable in class org.metaqtl.CMarkerSequence
  The indices of the markers on the first chromosome for the common sequences.
idx2 - Variable in class org.metaqtl.CMarkerSequence
  The indices of the marker on the second chromosome for the common sequences.
IGeneticMapProperties - Interface in org.thalia.bio.entity
  Class Description Here
ILGroupPosition - Interface in org.thalia.bio.util
  Class Description Here
IMetaAlgorithm - Interface in org.metaqtl
  This interface defines some methods which are common to data analysis algorithms.
IMetaQtlConstants - Interface in org.metaqtl
  This interface defines some global constants which are used by several classes of the package.
IMIN(int, int) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the min between `a` and `b`
incms - Variable in class org.metaqtl.CMarkerSequence
indexx(int, double[], int[]) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Sort the given array of double arrin[1..n] without destroying it and returns the sorted indices of the array elements into indx[1..n].
Individual - Class in org.thalia.bio.entity
  Class Description Here
Individual() - Constructor for class org.thalia.bio.entity.Individual
Individual(String, IBioEntity) - Constructor for class org.thalia.bio.entity.Individual
INDIVIDUAL - Static variable in interface org.thalia.bio.IBioEntityTypes
  The integer code for an individual entity
IndividualContainer - Class in org.thalia.bio.entity
  Class Description Here
IndividualContainer() - Constructor for class org.thalia.bio.entity.IndividualContainer
IndividualContainer(String, IBioEntity) - Constructor for class org.thalia.bio.entity.IndividualContainer
individuals() - Method in class org.thalia.bio.entity.IndividualContainer
individuals() - Method in interface org.thalia.bio.IBioPopulation
InfoMap - Class in org.metaqtl.main
InfoMap() - Constructor for class org.metaqtl.main.InfoMap
init(Graphics2D, ChromGraph[]) - Method in class org.metaqtl.graph.MetaGraph
initCmdLineParser() - Method in class org.metaqtl.main.MetaMain
initEM(double[], double[], EMResult, Random) - Static method in class org.metaqtl.algo.EMAlgorithm
  Initializes the EM algorithm by randomly assigning observations to the clusters and do one M-Step to compute the first values of the parameters.
initNodeIdx() - Method in class org.metaqtl.Tree
initPalettes() - Static method in class org.metaqtl.graph.MetaGraphPar
initProbaPalette() - Static method in class org.metaqtl.graph.MetaGraphPar
initQTLPalette() - Static method in class org.metaqtl.graph.MetaGraphPar
initQTLPalette(int) - Static method in class org.metaqtl.graph.MetaGraphPar
initReverse() - Method in class org.metaqtl.Tree
intScale - Variable in class org.metaqtl.Qtl.QTLProj
  The scale ratio between the original flanking marker interval and the one on the map used for projection.
IOntologyTermProperties - Interface in org.thalia.bio
IRISe - Static variable in interface org.thalia.bio.IBioCrossTypes
IRISi - Static variable in interface org.thalia.bio.IBioCrossTypes
isAssignableEntities(IResource, IBioEntity[]) - Static method in class org.thalia.bio.util.ResourceBioEntityQuery
  Returns true if all elements of entities are included in the resource.
isAssignableEntity(IResource, IBioEntity) - Static method in class org.thalia.bio.util.ResourceBioEntityQuery
  Returns true if the resource contains the given entity.
isConnected(int) - Method in class org.metaqtl.ChromCluster.ClusterGraph
  Test if the graph is connected
isConnected(int) - Method in class org.metaqtl.ChromCluster
  Tests if the cluster of chromosome is connected using a graph approach.
isDubiousLocus(IBioLocus) - Method in class org.metaqtl.ChromCluster
  If a list of dubious markers has been set before then this routine checks if the given locus is not included into this list.
isDubiousOrderLocus(IBioLocus) - Static method in class org.metaqtl.util.LocusProperties
  Returns true if the given locus has a property order.dubious set to one, false otherwise
isIgnore() - Method in class org.metaqtl.Qtl
  This methods returns true if the QTL must be ignored.
isLoggerEnable() - Method in class org.metaqtl.algo.MetaAlgorithm
ISWAP(int[], int, int) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Swaps elements i and j in a.
iterate(double[], double[], EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  This method performs one iteration of the EM-algorithm.

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